Re: [AMBER-Developers] mmpbsa tests (perl and python)

From: Mengjuei Hsieh <>
Date: Mon, 29 Mar 2010 17:57:03 -0700

On Mon, Mar 29, 2010 at 07:13:49PM -0400, Jason Swails wrote:
> As an update to this, I'm finding some weird timings with PB when run
> through our script. Below is the input file being printed by our
> script, so maybe someone more familiar with PBSA can enlighten me as
> to which variables I am setting that is killing the performance.
> Here is the input file:
> When istrng is set to 0, this will finish 1 frame in 1.613 minutes.
> When istrng is 100.0 (mM), 1 frame takes 20.057 minutes (I'm not sure
> which revision this started happening in, but it's relatively recent).

Hi, this sounds very interesting and we are intrigued by this
kind of performance difference. Can you send me a test case
so that I can reproduce the problem? I'll tehn report to recent
PBSA revision contributors.

Mengjuei Hsieh, Luo Research Group, Molecular Biology & Biochemistry,
University of California Irvine.
AMBER-Developers mailing list
Received on Mon Mar 29 2010 - 18:00:02 PDT
Custom Search